TFBSs tend to appear at fixed distance in the TEs that we studied. The case of MER41B is reported as an example. In A is shown the logo of ERα ChIP-seq regions carrying GATA-3 and ERR at the fixed distance of 24 nts (measured from start to start of these motifs). The multi-alignment of these regions is shown in B, together with genomic location and associated TE. C: distance distribution between GATA-3 and ERR in ERα ChIP-seq peaks. Notice that in all the three insets of the figure the reverse complement of the logo usually reported by Transfac is used.
Testori et al. BMC Genomics 2012 13:400 doi:10.1186/1471-2164-13-400